ggepitracks3: Plot Epigenetics Tracks for NGS Data using ggplot2 (version...
In liuyujie0136/tinyfuncr: tiny R functions

ggepitracks3

R Documentation

Plot Epigenetics Tracks for NGS Data using ggplot2 (version 3)

Description

Plot genome tracks for NGS data using ggplot2, resembling GBrowse style. Supporting coverage data in bigWig or bedGraph format from RNA-seq, sRNA-seq, BS-seq, ChIP-seq, RIP-seq, GRO-seq, NET-seq, DNase-seq, MNase-seq, ATAC-seq, SHAPE-seq etc. Especially optimized for BS-seq data in single-base resolution. Requires bigWigToBedGraph and bedtools on Linux.

Usage

ggepitracks3(
  locus_file,
  track_conf,
  bsseq_conf = NULL,
  gene_model,
  ann_region = NULL,
  ann_color = "#FFC1254D",
  out_dir = "out",
  height = NULL,
  width = 80
)

Arguments

`locus_file`	BED file containing locus to plot. For each line, TAB-delimited information should contain: <chr>, <start>, <end>, <locus_name>, without header.
`track_conf`	Configuration file containing track info. For each line, TAB-delimited information should contain: <track_name>, <track_type>, <track_bw/bg>, <y_min>, <y_max>, <color>, <group>, without header. NOTE: If you write "BS-seq" in "<track_type>", provide mC type (one of CG, CHG, CHH, All) to plot in "<track_bw/bg>" and provide detailed info in `bsseq_conf`, "<color>" is ignored in BS-seq tracks. "<group>" is currently unused.
`bsseq_conf`	Configuration file of BS-seq track. If there is no BS-seq track to plot, keep `NULL`. For each line, TAB-delimited information should contain: <track_name>, <CG_bw/bg>, <CHG_bw/bg>, <CHH_bw/bg>, <C_context_file>, without header. "<track_name>" here should be the same as in `track_conf`. If you choose only one mC type to plot, you can keep the column of other files as "NA", but provide all the bigWig files may be safe. "<C_context_file>" can be "NA" to ignore drawing C context track (currently unused).
`gene_model`	BED file containing all elements of gene and/or TE model, generated by `⁠[tinyfuncr::extractPos]⁠`
`ann_region`	BED file of annotation regions. If not provided, no annotation will be added. For each line, TAB-delimited information should contain: <chr>, <start>, <end>, <annotation_name>, without header. <annotation_name> could be empty but the last TAB should be kept.
`ann_color`	Color of annotated regions, defalut "#FFC1254D" (i.e., "goldenrod1", alpha 30)
`out_dir`	Path to output directory, will be created if not exist, default "out/". Output plots in PDF format will be saved as <out_dir>/<locus_name>.pdf
`height`	Plot height, in "mm", defalut 6*ntracks+10
`width`	Plot width, in "mm", defalut 80